I've already upgraded Anaconda and ran the command as just "activate salmon" instead of "conda activate salmon".
The file has also been removed from the bash_profile as recommended in the salmon notes.

conda activate salmon
CommandNotFoundError: Your shell has not been properly configured to use 'conda activate'.
If your shell is Bash or a Bourne variant, enable conda for the current user with
$ echo ". /anaconda3/etc/profile.d/conda.sh" >> ~/.bash_profile
or, for all users, enable conda with
$ sudo ln -s /anaconda3/etc/profile.d/conda.sh /etc/profile.d/conda.sh
The options above will permanently enable the 'conda' command, but they do NOT
put conda's base (root) environment on PATH. To do so, run
$ conda activate
in your terminal, or to put the base environment on PATH permanently, run
$ echo "conda activate" >> ~/.bash_profile
Previous to conda 4.4, the recommended way to activate conda was to modify PATH in
your ~/.bash_profile file. You should manually remove the line that looks like
export PATH="/anaconda3/bin:$PATH"
^^^ The above line should NO LONGER be in your ~/.bash_profile file! ^^^